/usr/share/ray/scripts/illumina-split-linked-sequences-fastq.py is in ray-extra 2.3.1-5.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 | #!/usr/bin/python
import sys
fastqFile=sys.argv[1]
adaptorSequence=sys.argv[2]
out=open(fastqFile+".fasta","w+")
i=0
id1=""
seq1=""
seq2=""
for line in open(fastqFile):
if i==0:
id1=line.strip().replace("@",">")
elif i==1:
seq1=line.strip()
elif i==4:
id2=line.strip().replace("@",">")
elif i==5:
seq2=line.strip()
tokens1=seq1.split(adaptorSequence)
tokens2=seq2.split(adaptorSequence)
if len(tokens1)>1:
seq1=tokens1[0]
if len(tokens2)>1:
seq2=tokens2[0]
out.write(id1+" length="+str(len(seq1))+"\n")
out.write(seq1+"\n")
out.write(id2+" length="+str(len(seq2))+"\n")
out.write(seq2+"\n")
i+=1
if i==8:
i=0
out.close()
|